Ab Initio Molecular Dynamics Simulations to Interpret the Molecular Fragmentation Induced in Deoxyribose by Synchrotron Soft X-Rays

Abstract

It has been suggested that core ionization in DNA atoms could induce complex, irreparable damage. Synchrotron soft X-rays have been used to probe the damage induced by such events in thin films of DNA components. In a complementary approach, we investigate the fragmentation dynamics following a carbon or oxygen K-shell ionization in 2-deoxy-D-ribose (DR), a major component in the DNA chain. Core ionization of the sugars hydration layer is also studied. To that aim, we use state-of-the-art ab initio Density Functional Theory-based Molecular Dynamics (MD) simulations. The ultrafast dissociation dynamics of the core ionized molecule, prior Auger decay, is modeled for about 10 fs. We show that the core-ionization of oxygen atoms within DR or its hydration layer may induce proton transfers towards nearby molecules, before Auger decay. In a second step, we model an Auger effect occurring either at the beginning or at the end of the core–hole dynamics. Two electrons are removed from the deepest valence molecular orbitals localized on the initially core-ionized oxygen atom (O*), and this electronic state is propagated by means of Ehrenfest MD. We show an ultrafast dissociation of the DR2+ molecule C-O* bonds, which, in most cases, seems independent of the time at which Auger decay occurs.

Ultrafast fragmentation of highly-excited doubly-ionized deoxyribose: role of the liquid water environment

“…The resulting DR hydration is described elsewhere. 79 The final equilibration configurations (atomic positions and velocities) are the initial configurations ( t = 0) for the doubly ionized system Ehrenfest molecular dynamics. The isolated DR conformations is similar to that of isomer 2 .…”

Ab initio molecular dynamics calculations on electron ionization induced fragmentations of C4F7N and C5F10O for understanding their decompositions under discharge conditions

“…For a more detailed description of the working mechanisms, the reader is referred to the original literature. 27 It is worth noting that the AIMD simulation is also able to reproduce the molecular fragmentation 43,44 or dissociative electron attachment for mass spectrometry 45 when extra electrons are introduced into a system. However, it is not the case discussed in this paper; we treat the system as spontaneously ionized.…”

Investigating electron-induced dissociation dynamics in the organometallic precursor Fe(CO)5: a nonadiabatic molecular dynamics approach

“…Employing rigorous quantum-mechanical frameworks such as TDDFT allows for detailed insights into these processes. TDDFT is particularly suited for investigating relatively small molecular systems comprising the few hundred atoms or fewer, with dynamics unfolding on the subpicosecond time scale [31][32][33].…”